But even the departmental hierarchy concedes that there is still much unhappiness among the rank-and-file over how they have been treated since 2014.

Departmental Secretary Daryl Quinlivan conceded on Monday morning that the three-year dispute had been "intense, frustrating and emotive" while announcing the result of the ballot.

The new deal was accepted by 63 per cent of an 85 per cent turnout of eligible public servants, who have not had a general pay rise since 2013.

They will now get a deal worth an average of 2 per cent a year for three years but there will be no back pay, which is banned as part of the Coalition's Abott-era public sector bargaining policy.

Mr Quinlivan reflected on Monday morning on the three years of industrial strife at his department.

"The last three years of bargaining have been intense, sometimes frustrating and emotive for a lot our employees," he wrote.

"We've had a long journey toward a successful agreement, and I know not everyone will be happy with the outcome.

"No matter how you voted, I think we can all agree that having bargaining behind us is an opportunity to refocus on our strategic priorities."

The main workplace union, the CPSU, said the marathon struggle demonstrated the failure of the government in managing its public service workforce.

"It's better news for Agriculture staff that there's finally a resolution to this protracted dispute, but the fact it took five ballots to get there underlines the Turnbull government's abject failure over public sector bargaining," CPSU national secretary Nadine Flood said.

"This agreement is far from perfect and is still far less than what staff deserve, but it's a marked improvement on what's been previously offered.

"It is fundamentally unfair that staff will not get back-pay because it's absolutely not their fault this has dragged on so long."